diff --git a/CHANGES/v2.5.md b/CHANGES/v2.5.md index eefd78c678e3e30a7cbfc7e4043ce989deec0616..bd29ab92d193e013ec9d62610b67798036f67d45 100644 --- a/CHANGES/v2.5.md +++ b/CHANGES/v2.5.md @@ -47,8 +47,8 @@ Changes from version 2.4 which are relevant for users: - \ref pdbrenumber (see \issue{371}). - Changes in the ISDB module - - \ref CS2BACKBONE is now mpi parallelised in particular with DOSCORE and CAMSHIFT - - \ref SAXS has an additional implementation based on bessel functions that can be faster for large systems (new keyword BESSEL) + - \ref CS2BACKBONE is now mpi parallelized in particular with DOSCORE and CAMSHIFT + - \ref SAXS has an additional implementation based on Bessel functions that can be faster for large systems (new keyword BESSEL) - \ref SAXS keyword SCEXP has been renamed into SCALEINT - \ref METAINFERENCE and all related methods has a new keyword REGRES_ZERO to scale data using a linear scale fit - \ref CALIBER new bias to perform Maximum Caliber replica-averaged restrained simulations @@ -68,12 +68,12 @@ Changes from version 2.4 which are relevant for users: - Other changes: - \ref METAD there is a new FLYING_GAUSSIAN keyword to activate the flying gaussian methods by Spiwok (contributed by Spiwok and Hozzova) - \ref EXTERNAL can now SCALE the input grid. This allows for more flexibility without modifying the grid file. - - \ref ALPHABETA can now combine dihedrals with different coefficients + - \ref ALPHABETA can now combine dihedral angles with different coefficients - \ref INCLUDE can now be used also before setup actions. - - \ref CENTER can now be computed using trigonometric functions (PHASES) to simplify its calculation with PBCs. + - \ref CENTER can now be computed using trigonometric functions (PHASES) to simplify its calculation with periodic boundary conditions. - Libmatheval is not used anymore. \ref MATHEVAL (and \ref CUSTOM) are still available but employ an internal implementation of the lepton library. - Functions available in libmatheval and absent in the original lepton library have been added so as to have backward compatbility. + Functions available in libmatheval and absent in the original lepton library have been added so as to have backward compatibility. `atan2(y,x)` function has also been added. Notice that MATHEVAL (and CUSTOM) \ref switchingfunction "switching functions" using the lepton library have been further optimized with respect to PLUMED 2.4. @@ -82,7 +82,7 @@ Changes from version 2.4 which are relevant for users: - \ref MOLINFO now allows selecting atoms from chains with a numeric ID (see \issue{320}). - Removed the patch for GMX 5.1.4 - \ref RMSD calculation has been optimized. This should positively affect the performances of CVs where - many RMSDs are computed on small groups of atoms, such as secondary structure variables. + many RMSD values are computed on small groups of atoms, such as secondary structure variables. - In \ref METAD, when using a bias factor equal to one (no bias) the `rct` component is set to zero rather than to one. - New shortcuts are available for selecting atoms: `@allatoms` and `@mdatoms` (see \ref atomSpecs). - When using \ref MOLINFO, also the following shortcuts are available for selecting atoms: `@nucleic`, `@protein`, `@water`, `@ions`, `@hydrogens`, `@nonhydrogens`. @@ -110,8 +110,8 @@ Changes from version 2.4 which are relevant for developers: - Exception class has been rewritten to allow more extensive messages. Now also function name is shown. - On linux, library is linked with `-Bsymbolic`. - A small number of header files is installed -- When launching `plumed`, flags `--no-mpi` and `--mpi` can appear multiple times. The last appearence is the effective one. -- Internal blas and lapack libraries updated to gromacs 2018. +- When launching `plumed`, flags `--no-mpi` and `--mpi` can appear multiple times. The last appearance is the effective one. +- Internal BLAS and LAPACK libraries updated to gromacs 2018. - Choosing `./configure --prefix=$PWD` does not lead anymore to deletion of all header files. - Runtime loader in `Plumed.c` now works also when linked without `-rdynamic` (that is, its names are not exported). Notice that all the combinations are expected to